LeDock

LeDock is a simple proprietary molecular docking software that can be used for docking of ligands with protein target.[1] LeDock supports running on 64-bit Linux, macOS, and 32-bit and 64-bit Windows.

LeDock
Developer(s)Lephar
Operating systemCross-platform
TypeMolecular docking
Websitewww.lephar.com/software.htm

Introduction

LeDock is based on simulated annealing and evolutionary optimization of the ligand pose and its rotatable bonds, using a physics/knowledge-based scoring scheme derived from years of prospective virtual screening campaigns.[2][3][4][5][6]

Performance

LeDock had a good performance in a recent comprehensive evaluation of docking programs on a diverse set of 2002 protein-ligand complexes.[7] It has high accuracy in pose prediction, saving calculating time, and user friendly for both virtual screening and hit elaboration.

See also

References
  1. "User Guide for LeDock" (PDF).
  2. Zhao, Hongtao; Huang, Danzhi (2011-06-17). "Hydrogen Bonding Penalty upon Ligand Binding". PLOS ONE. 6 (6): e19923. doi:10.1371/journal.pone.0019923. ISSN 1932-6203. PMC 3117785. PMID 21698148.
  3. Zhao, Hongtao; Huang, Danzhi; Caflisch, Amedeo (2012-11-01). "Discovery of Tyrosine Kinase Inhibitors by Docking into an Inactive Kinase Conformation Generated by Molecular Dynamics". ChemMedChem. 7 (11): 1983–1990. doi:10.1002/cmdc.201200331. ISSN 1860-7187. PMID 22976951.
  4. Zhao, Hongtao; Caflisch, Amedeo (2013-10-15). "Discovery of ZAP70 inhibitors by high-throughput docking into a conformation of its kinase domain generated by molecular dynamics". Bioorganic & Medicinal Chemistry Letters. 23 (20): 5721–5726. doi:10.1016/j.bmcl.2013.08.009. PMID 23993776.
  5. Zhao, Hongtao; Caflisch, Amedeo (2014-03-15). "Discovery of dual ZAP70 and Syk kinases inhibitors by docking into a rare C-helix-out conformation of Syk". Bioorganic & Medicinal Chemistry Letters. 24 (6): 1523–1527. doi:10.1016/j.bmcl.2014.01.083. PMID 24569110.
  6. Zhao, Hongtao; Gartenmann, Lisa; Dong, Jing; Spiliotopoulos, Dimitrios; Caflisch, Amedeo (2014-06-01). "Discovery of BRD4 bromodomain inhibitors by fragment-based high-throughput docking". Bioorganic & Medicinal Chemistry Letters. 24 (11): 2493–2496. doi:10.1016/j.bmcl.2014.04.017. PMID 24767840.
  7. Wang, Zhe (2016). "Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power". Physical Chemistry Chemical Physics. 18 (18): 12964–12975. doi:10.1039/C6CP01555G. PMID 27108770.
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